Comprehensive genome methylation analysis in bladder cancer;identification and validation of novel methylated genes and application of these as urinary tumor markers - Abstract

Dept. of Molecular Medicine, University of Aarhus, Denmark.


Epigenetic alterations are common and can now be addressed in a parallel fashion. We investigated the methylation in bladder cancer with respect to location in genome, consistency, variation in metachronous tumors, impact on transcripts, chromosomal location, and usefulness as urinary markers.

A microarray assay was utilized to analyze methylation in 56 samples. Independent validation was performed in 63 samples by a PCR based method and bisulfite sequencing. The methylation levels in 174 urine specimens were quantified. Transcript levels were analyzed using expression microarrays, and pathways using dedicated software.

Global methylation patterns were established within and outside CpG-islands. We validated methylation of the eight tumor markers genes ZNF154 (p< 0.0001), HOXA9 (p< 0.0001), POU4F2 (p< 0.0001), EOMES (p=0.0005), ACOT11 (p=0.0001), PCDHGA12 (p=0.0001), CA3 (p=0.0002), and PTGDR (p=0.0110), the candidate marker of disease progression TBX4 (p< 0.04), and other genes with stage specific methylation. The methylation of metachronous tumors was stable and targeted to certain pathways. The correlation to expression was not stringent. Chromosome 21 showed most differential methylation (p< 0.0001) and specifically hypomethylation of keratins, which together with keratin like proteins were epigenetically regulated. In DNA from voided urine we detected differential methylation of ZNF154 (p< 0.0001), POU4F2 (p< 0.0001), HOXA9 (p< 0.0001), and EOMES (p< 0.0001) achieving 84% sensitivity and 96% specificity.

We initiated a detailed mapping of the methylome in metachronous bladder cancer. Novel genes with tumor, chromosome, as well as pathway specific differential methylation in bladder cancer were identified. The methylated genes were promising cancer markers for early detection of bladder cancer.

Written by:
Reinert T, Modin C, Mansilla Castano F, Lamy P, Wojdacz TK, Hansen LL, Wiuf C, Borre M, Dyrskjøt L, Orntoft TF.   Are you the author?

Reference: Clin Cancer Res. 2011 Jul 25. Epub ahead of print.
doi: 10.1158/1078-0432.CCR-10-2659

PubMed Abstract
PMID: 21788354 Bladder Cancer Section